Sunday, February 15, 2015

Health Variant Report


The tool is not intended to provide any health interpretations. If you notice the result requires health attention then please visit a physician and do proper tests and confirm.


Variant Report takes the risk information from a configurable file 'app.conf' and generates report with health related information from autosomal files. Currently, 23andMe, FTDNA and Ancestry files are supported.

Prerequisites: Microsoft .Net Framework 4.0

Usage: Edit the app.conf in a notepad (or any text editor), add the required risk alleles and generate the report. The app.conf is a comma separated file with the following fields. Category, Gene, RSID, Risk Allele, Notes and any line starting with # is a comment.

Screenshot:





Download : Variant Report.zip (111 KB)

Source Code at GitHub.

Change Log
Version 1.0
  • Initial Release.

Wednesday, January 28, 2015

The Imputer

If you had done your autosomal DNA testing and you want to know the genotypes of all possible untested SNPs, this is the tool. The Imputer accurately predicts all genotypes of untested SNPs. The tool supports FTDNA, 23andMe and Ancestry autosomal build 37 files.

Usage: Select the autosomal DNA input file, enter the output filename and select an option for what to do for unidentified allele, then click 'Impute'.

Prerequisites: Microsoft .Net Framework 4.0

Screenshot:

Download : The Imputer.zip (8.31 GB)

To avoid download failures on large files from Google drive, make sure you use a download manager. Please refer to post, Downloading large files from Google Drive using Download Manager for a quick tutorial.

Source Code at GitHub

Change Log
    Version 1.0
    • Initial Release.

    Tuesday, January 27, 2015

    Assembly Converter

    Converts human genome coordinates from one assembly to another on raw autosomal DNA files. The tool supports FTDNA, Ancestry and 23andMe autosomal files. This tool replaces the obsolete build converter.

    Usage: Select the autosomal DNA input file, appropriate LiftOver chain file and enter the output filename, then click 'Convert'. The output will be in exact same format as the input, except the coordinates changed.

    Prerequisites: Microsoft .Net Framework 4.0

    Screenshot:

    Download : Assembly Converter.exe (385 Kb)

    Conversion LiftOver Chain Files
    Hg38/GRCh38 to Hg19/GRCh37hg38ToHg19.over.chain.gz (1.2 MB)
    Hg19/GRCh37 to Hg38/GRCh38hg19ToHg38.over.chain.gz (222 Kb)
    Hg19/GRCh37 to Hg18hg19ToHg18.over.chain.gz (221 Kb)
    Hg18 to Hg38/GRCh38hg18ToHg38.over.chain.gz (336 Kb)
    Hg18 to Hg19/GRCh37hg18ToHg19.over.chain.gz (137 Kb)
    The complete list of chain files for all human genome assemblies can be downloaded from here.

    Source Code at GitHub

    Change Log
      Version 1.0
      • Initial Release.

      Wednesday, January 21, 2015

      SNP Prophet

      If you had done your autosomal DNA testing and you want to know the genotype of an untested SNP, this is the tool. SNP prophet predicts your genotype for an untested SNP using your autosomal DNA. It has an offline version and an online version.The offline is huge but does not require any internet, nor depends on 3rd party services to be available on the internet, since everything it requires will be present in your computer. The online version however is extremely less is size but entirely depends on 3rd party APIs (OpenSNP's JSON and DAS) and their service availability. The tool supports FTDNA, Ancestry and 23andMe files.

      Usage: Select the autosomal DNA file, enter the SNP you want to know it's genotype and click 'Find GenoType'. The total process for both online and offline can take sometimes 5 to 10 minutes.

      Prerequisites: Microsoft .Net Framework 4.0

      Screenshot:

      Download :
      To avoid download failures on large files from Google drive, make sure you use a download manager. Please refer to post, Downloading large files from Google Drive using Download Manager for a quick tutorial.

      Source Code:

      Change Log
        Version 1.0
        • Initial Release.

        Tyrolean Ancient DNA

        The Tyrolean Iceman, a 5300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Oetztal Alps. The authors sequenced the complete genome of the Iceman. The authors had mentioned in the paper that they were able to extract 125,729 SNPs from all samples. I was able to convert only 2 samples ERR107308 and ERR107309 due to technical limitations.

        Download: 
        Reference:
        Keller, Andreas, et al. "New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing." Nature communications 3 (2012): 698.

        Data Used